Index B | C | D | F | G | H | L | M | P | R | S | T | U | W B bcr_summary_csv() (in module scab.vdj) build_synthesis_constructs() (in module scab.vdj) C cdr3_length_barplot() (in module scab.pl) cellhash_ridge() (in module scab.pl) classify_specificity() (in module scab.tools.specificity) clonify() (in module scab.tools.clonify) (in module scab.vdj) combat() (in module scab.tools.batch_correction) concat() (in module scab.io) D demultiplex() (in module scab.tools.cellhashes) dimensionality_reduction() (in module scab.tools.embeddings) doubletdetection() (in module scab.pp) F feature_kde() (in module scab.pl) feature_ridge() (in module scab.pl) filter_and_normalize() (in module scab.pp) G germline_use_barplot() (in module scab.pl) get() (scab.models.lineage.LineageAssignment method) get_pairing_info() (in module scab.vdj) H harmony() (in module scab.tools.batch_correction) L Lineage (class in scab.models.lineage) lineage_donut() (in module scab.pl) LineageAssignment (class in scab.models.lineage) LineageSummary (class in scab.models.lineage) load() (in module scab.io) M merge() (in module scab.vdj) merge_bcr() (in module scab.vdj) merge_tcr() (in module scab.vdj) mnn() (in module scab.tools.batch_correction) module scab.io scab.models.lineage scab.pl scab.pp scab.tools.batch_correction scab.tools.cellhashes scab.tools.clonify scab.tools.embeddings scab.tools.specificity scab.vdj P pairwise_distance() (in module scab.tools.clonify) pca() (in module scab.tools.embeddings) R read() (in module scab.io) read_10x_mtx() (in module scab.io) remove_doublets() (in module scab.pp) S save() (in module scab.io) scab.io module scab.models.lineage module scab.pl module scab.pp module scab.tools.batch_correction module scab.tools.cellhashes module scab.tools.clonify module scab.tools.embeddings module scab.tools.specificity module scab.vdj module scanorama() (in module scab.tools.batch_correction) scrublet() (in module scab.pp) T to_fasta() (in module scab.vdj) U umap() (in module scab.tools.embeddings) W write() (in module scab.io)